AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1422980


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1422980 MtrunA17_Chr7g0272591 94.030 67 2 2 1 66 1 66 6.50e-27 102
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 17 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCAAATTTATCTTCTTTCA+TGG 0.231855 tig0025496:+62268 None:intergenic
ATTAGGTGATGAATAAATTA+CGG 0.358514 tig0025496:-62305 Msa1422980:intron
GAAACTAACGGACCGCTTAA+AGG 0.384520 tig0025496:+63248 None:intergenic
ATCATCATCATCAAGAAATA+TGG 0.391274 tig0025496:-63334 Msa1422980:CDS
CTCCACCTCATCGCTGAACC+TGG 0.430406 tig0025496:+63193 None:intergenic
CAGGTTCAGCGATGAGGTGG+AGG 0.523948 tig0025496:-63192 Msa1422980:CDS
CGCCAGGTTCAGCGATGAGG+TGG 0.525195 tig0025496:-63195 Msa1422980:CDS
AGCACGAGAGTAGGCTTCAG+TGG 0.544891 tig0025496:-63284 Msa1422980:CDS
GGAAGCAGAAGCACGAGAGT+AGG 0.557076 tig0025496:-63293 Msa1422980:CDS
AAAGCAGCAAGAAAAGCGCC+AGG 0.558816 tig0025496:-63211 Msa1422980:CDS
TCAAGAAATATGGTCGGAGA+CGG 0.582861 tig0025496:-63324 Msa1422980:CDS
TGGTCGGAGACGGAGAGTAA+CGG 0.584768 tig0025496:-63314 Msa1422980:CDS
TTCTTGTTGTTGGAAACTAA+CGG 0.585089 tig0025496:+63236 None:intergenic
AAGCGCCAGGTTCAGCGATG+AGG 0.642839 tig0025496:-63198 Msa1422980:CDS
TCATCATCAAGAAATATGGT+CGG 0.656566 tig0025496:-63330 Msa1422980:CDS
GGCTTCAGTGGATCACTAAG+CGG 0.669801 tig0025496:-63272 Msa1422980:CDS
TCACTAAGCGGACCTTTAAG+CGG 0.676159 tig0025496:-63260 Msa1422980:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTATTTTAATGAATTGTAA+AGG + tig0025496:62762-62781 None:intergenic 15.0%
!!! TTATCGTAAAAATCATTTTA+TGG + tig0025496:62961-62980 None:intergenic 15.0%
!! TGTGAATAATTTACTTAATA+CGG - tig0025496:63027-63046 Msa1422980:intron 15.0%
!! GGTTAAACATATAAAAAAAA+AGG - tig0025496:63094-63113 Msa1422980:intron 15.0%
!! AAGGAAATTATTAACATAAA+AGG - tig0025496:63113-63132 Msa1422980:intron 15.0%
!!! GTTATTTTAATGAATTGTAA+AGG + tig0025496:62762-62781 None:intergenic 15.0%
!!! TTATCGTAAAAATCATTTTA+TGG + tig0025496:62961-62980 None:intergenic 15.0%
!! TGTGAATAATTTACTTAATA+CGG - tig0025496:63027-63046 Msa1422980:intron 15.0%
!! GGTTAAACATATAAAAAAAA+AGG - tig0025496:63094-63113 Msa1422980:intron 15.0%
!! AAGGAAATTATTAACATAAA+AGG - tig0025496:63113-63132 Msa1422980:intron 15.0%
!! CACAAAAATAGTCATATTTA+TGG - tig0025496:62908-62927 Msa1422980:intron 20.0%
!! TAATACGGTCAATAAAAATT+AGG - tig0025496:63042-63061 Msa1422980:intron 20.0%
!! AATACGGTCAATAAAAATTA+GGG - tig0025496:63043-63062 Msa1422980:intron 20.0%
!! TTACATTATATGATTGTGAT+CGG + tig0025496:63250-63269 None:intergenic 20.0%
!!! TGACCTTGTTAATTTTTATT+AGG - tig0025496:63312-63331 Msa1422980:CDS 20.0%
!! TCACCTAATAAAAATTAACA+AGG + tig0025496:63318-63337 None:intergenic 20.0%
!! ATTAGGTGATGAATAAATTA+CGG - tig0025496:63329-63348 Msa1422980:CDS 20.0%
!! CACAAAAATAGTCATATTTA+TGG - tig0025496:62908-62927 Msa1422980:intron 20.0%
!! TAATACGGTCAATAAAAATT+AGG - tig0025496:63042-63061 Msa1422980:intron 20.0%
!! AATACGGTCAATAAAAATTA+GGG - tig0025496:63043-63062 Msa1422980:intron 20.0%
!! TTACATTATATGATTGTGAT+CGG + tig0025496:63250-63269 None:intergenic 20.0%
!!! TGACCTTGTTAATTTTTATT+AGG - tig0025496:63312-63331 Msa1422980:CDS 20.0%
!! TCACCTAATAAAAATTAACA+AGG + tig0025496:63318-63337 None:intergenic 20.0%
!! ATTAGGTGATGAATAAATTA+CGG - tig0025496:63329-63348 Msa1422980:CDS 20.0%
! ATCATCATCATCAAGAAATA+TGG - tig0025496:62300-62319 Msa1422980:CDS 25.0%
!! ATTTTACTCGTTTCCTAATA+TGG + tig0025496:62537-62556 None:intergenic 25.0%
! TATACAAGAAACTAATGCTA+TGG - tig0025496:62607-62626 Msa1422980:intron 25.0%
!!! TATCATTTGACTTTTGTTTG+CGG + tig0025496:62854-62873 None:intergenic 25.0%
!! TCGGCATGTAATTAATTTTT+AGG + tig0025496:63231-63250 None:intergenic 25.0%
! GTGGAATAAAAATTAACATG+TGG + tig0025496:63280-63299 None:intergenic 25.0%
! ATCATCATCATCAAGAAATA+TGG - tig0025496:62300-62319 Msa1422980:CDS 25.0%
!! ATTTTACTCGTTTCCTAATA+TGG + tig0025496:62537-62556 None:intergenic 25.0%
! TATACAAGAAACTAATGCTA+TGG - tig0025496:62607-62626 Msa1422980:intron 25.0%
!!! TATCATTTGACTTTTGTTTG+CGG + tig0025496:62854-62873 None:intergenic 25.0%
!! TCGGCATGTAATTAATTTTT+AGG + tig0025496:63231-63250 None:intergenic 25.0%
! GTGGAATAAAAATTAACATG+TGG + tig0025496:63280-63299 None:intergenic 25.0%
TCATCATCAAGAAATATGGT+CGG - tig0025496:62304-62323 Msa1422980:intron 30.0%
!! TTCTTGTTGTTGGAAACTAA+CGG + tig0025496:62401-62420 None:intergenic 30.0%
AATGCTATGGTAAGCTATTA+TGG - tig0025496:62620-62639 Msa1422980:intron 30.0%
! TCGCTGTGTAATAACTTTTA+CGG - tig0025496:62714-62733 Msa1422980:intron 30.0%
! TAAAGGTGTGTTAAAATGCA+TGG + tig0025496:62745-62764 None:intergenic 30.0%
!! AAGAGAGAAGTATTACACAA+TGG - tig0025496:62808-62827 Msa1422980:intron 30.0%
AAATACTAACTGATGTCTCT+GGG + tig0025496:63207-63226 None:intergenic 30.0%
AAAATACTAACTGATGTCTC+TGG + tig0025496:63208-63227 None:intergenic 30.0%
AAGGTCAGTATATTTGAAAG+TGG + tig0025496:63299-63318 None:intergenic 30.0%
TCATCATCAAGAAATATGGT+CGG - tig0025496:62304-62323 Msa1422980:intron 30.0%
!! TTCTTGTTGTTGGAAACTAA+CGG + tig0025496:62401-62420 None:intergenic 30.0%
AATGCTATGGTAAGCTATTA+TGG - tig0025496:62620-62639 Msa1422980:intron 30.0%
! TCGCTGTGTAATAACTTTTA+CGG - tig0025496:62714-62733 Msa1422980:intron 30.0%
! TAAAGGTGTGTTAAAATGCA+TGG + tig0025496:62745-62764 None:intergenic 30.0%
!! AAGAGAGAAGTATTACACAA+TGG - tig0025496:62808-62827 Msa1422980:intron 30.0%
AAATACTAACTGATGTCTCT+GGG + tig0025496:63207-63226 None:intergenic 30.0%
AAAATACTAACTGATGTCTC+TGG + tig0025496:63208-63227 None:intergenic 30.0%
AAGGTCAGTATATTTGAAAG+TGG + tig0025496:63299-63318 None:intergenic 30.0%
! GAAGTATTACACAATGGTAG+AGG - tig0025496:62814-62833 Msa1422980:intron 35.0%
AAAATTAGGGTCATGCTAAC+CGG - tig0025496:63056-63075 Msa1422980:intron 35.0%
! GAAGTATTACACAATGGTAG+AGG - tig0025496:62814-62833 Msa1422980:intron 35.0%
AAAATTAGGGTCATGCTAAC+CGG - tig0025496:63056-63075 Msa1422980:intron 35.0%
TCAAGAAATATGGTCGGAGA+CGG - tig0025496:62310-62329 Msa1422980:intron 40.0%
!!! GCTGCTTTTCTTCTTGTTGT+TGG + tig0025496:62411-62430 None:intergenic 40.0%
TGCGCAAGTTATTGTAGCTA+GGG + tig0025496:62665-62684 None:intergenic 40.0%
TCAAGAAATATGGTCGGAGA+CGG - tig0025496:62310-62329 Msa1422980:intron 40.0%
!!! GCTGCTTTTCTTCTTGTTGT+TGG + tig0025496:62411-62430 None:intergenic 40.0%
TGCGCAAGTTATTGTAGCTA+GGG + tig0025496:62665-62684 None:intergenic 40.0%
TCACTAAGCGGACCTTTAAG+CGG - tig0025496:62374-62393 Msa1422980:intron 45.0%
! GAAACTAACGGACCGCTTAA+AGG + tig0025496:62389-62408 None:intergenic 45.0%
! TCGAATGTTCTGGACCGAAA+CGG + tig0025496:62504-62523 None:intergenic 45.0%
CTGCGCAAGTTATTGTAGCT+AGG + tig0025496:62666-62685 None:intergenic 45.0%
TACACAATGGTAGAGGCAAG+TGG - tig0025496:62821-62840 Msa1422980:intron 45.0%
ACACAATGGTAGAGGCAAGT+GGG - tig0025496:62822-62841 Msa1422980:intron 45.0%
ATATGTTTAACCAGTGCCGC+AGG + tig0025496:63086-63105 None:intergenic 45.0%
!! GATGTCTCTGGGACACATAT+AGG + tig0025496:63196-63215 None:intergenic 45.0%
TCACTAAGCGGACCTTTAAG+CGG - tig0025496:62374-62393 Msa1422980:intron 45.0%
! GAAACTAACGGACCGCTTAA+AGG + tig0025496:62389-62408 None:intergenic 45.0%
! TCGAATGTTCTGGACCGAAA+CGG + tig0025496:62504-62523 None:intergenic 45.0%
CTGCGCAAGTTATTGTAGCT+AGG + tig0025496:62666-62685 None:intergenic 45.0%
TACACAATGGTAGAGGCAAG+TGG - tig0025496:62821-62840 Msa1422980:intron 45.0%
ACACAATGGTAGAGGCAAGT+GGG - tig0025496:62822-62841 Msa1422980:intron 45.0%
ATATGTTTAACCAGTGCCGC+AGG + tig0025496:63086-63105 None:intergenic 45.0%
!! GATGTCTCTGGGACACATAT+AGG + tig0025496:63196-63215 None:intergenic 45.0%
GGCTTCAGTGGATCACTAAG+CGG - tig0025496:62362-62381 Msa1422980:intron 50.0%
!! AAAGCAGCAAGAAAAGCGCC+AGG - tig0025496:62423-62442 Msa1422980:intron 50.0%
GTTTCGGTCCAGAACATTCG+AGG - tig0025496:62503-62522 Msa1422980:intron 50.0%
TATCACCGCCTCGAATGTTC+TGG + tig0025496:62514-62533 None:intergenic 50.0%
CGAGGCGGTGATACCATATT+AGG - tig0025496:62521-62540 Msa1422980:intron 50.0%
GGCTTCAGTGGATCACTAAG+CGG - tig0025496:62362-62381 Msa1422980:intron 50.0%
!! AAAGCAGCAAGAAAAGCGCC+AGG - tig0025496:62423-62442 Msa1422980:intron 50.0%
GTTTCGGTCCAGAACATTCG+AGG - tig0025496:62503-62522 Msa1422980:intron 50.0%
TATCACCGCCTCGAATGTTC+TGG + tig0025496:62514-62533 None:intergenic 50.0%
CGAGGCGGTGATACCATATT+AGG - tig0025496:62521-62540 Msa1422980:intron 50.0%
TGGTCGGAGACGGAGAGTAA+CGG - tig0025496:62320-62339 Msa1422980:intron 55.0%
! GGAAGCAGAAGCACGAGAGT+AGG - tig0025496:62341-62360 Msa1422980:intron 55.0%
AGCACGAGAGTAGGCTTCAG+TGG - tig0025496:62350-62369 Msa1422980:intron 55.0%
CGATGAGGTGGAGGATTACG+TGG - tig0025496:62451-62470 Msa1422980:intron 55.0%
CGTTCGCGATGACACCGTTT+CGG - tig0025496:62487-62506 Msa1422980:intron 55.0%
TCGGTCCAGAACATTCGAGG+CGG - tig0025496:62506-62525 Msa1422980:intron 55.0%
TGGTCGGAGACGGAGAGTAA+CGG - tig0025496:62320-62339 Msa1422980:intron 55.0%
! GGAAGCAGAAGCACGAGAGT+AGG - tig0025496:62341-62360 Msa1422980:intron 55.0%
AGCACGAGAGTAGGCTTCAG+TGG - tig0025496:62350-62369 Msa1422980:intron 55.0%
CGATGAGGTGGAGGATTACG+TGG - tig0025496:62451-62470 Msa1422980:intron 55.0%
CGTTCGCGATGACACCGTTT+CGG - tig0025496:62487-62506 Msa1422980:intron 55.0%
TCGGTCCAGAACATTCGAGG+CGG - tig0025496:62506-62525 Msa1422980:intron 55.0%
AAGCGCCAGGTTCAGCGATG+AGG - tig0025496:62436-62455 Msa1422980:intron 60.0%
CTCCACCTCATCGCTGAACC+TGG + tig0025496:62444-62463 None:intergenic 60.0%
CAGGTTCAGCGATGAGGTGG+AGG - tig0025496:62442-62461 Msa1422980:intron 60.0%
CATGCTAACCGGTGCTCCTG+CGG - tig0025496:63067-63086 Msa1422980:intron 60.0%
AAGCGCCAGGTTCAGCGATG+AGG - tig0025496:62436-62455 Msa1422980:intron 60.0%
CTCCACCTCATCGCTGAACC+TGG + tig0025496:62444-62463 None:intergenic 60.0%
CAGGTTCAGCGATGAGGTGG+AGG - tig0025496:62442-62461 Msa1422980:intron 60.0%
CATGCTAACCGGTGCTCCTG+CGG - tig0025496:63067-63086 Msa1422980:intron 60.0%
CGCCAGGTTCAGCGATGAGG+TGG - tig0025496:62439-62458 Msa1422980:intron 65.0%
! AACCAGTGCCGCAGGAGCAC+CGG + tig0025496:63078-63097 None:intergenic 65.0%
CGCCAGGTTCAGCGATGAGG+TGG - tig0025496:62439-62458 Msa1422980:intron 65.0%
! AACCAGTGCCGCAGGAGCAC+CGG + tig0025496:63078-63097 None:intergenic 65.0%
AACCGGTGCTCCTGCGGCAC+TGG - tig0025496:63073-63092 Msa1422980:intron 70.0%
AACCGGTGCTCCTGCGGCAC+TGG - tig0025496:63073-63092 Msa1422980:intron 70.0%
Chromosome Type Strat End Strand Name
tig0025496 gene 62275 63381 62275 ID=Msa1422980;Name=Msa1422980
tig0025496 mRNA 62275 63381 62275 ID=Msa1422980-mRNA-1;Parent=Msa1422980;Name=Msa1422980-mRNA-1;_AED=0.57;_eAED=0.58;_QI=0|0|0|0.5|0|0|2|0|80
tig0025496 exon 63187 63381 63187 ID=Msa1422980-mRNA-1:exon:2986;Parent=Msa1422980-mRNA-1
tig0025496 exon 62275 62322 62275 ID=Msa1422980-mRNA-1:exon:2985;Parent=Msa1422980-mRNA-1
tig0025496 CDS 63187 63381 63187 ID=Msa1422980-mRNA-1:cds;Parent=Msa1422980-mRNA-1
tig0025496 CDS 62275 62322 62275 ID=Msa1422980-mRNA-1:cds;Parent=Msa1422980-mRNA-1
Gene Sequence

>Msa1422980

ATGGAGATTAGTCAAGAGAAAGAGAATCATCATCATCAAGAAATATGGTCGGAGACGGAGAGTAACGGAAGCAGAAGCACGAGAGTAGGCTTCAGTGGATCACTAAGCGGACCTTTAAGCGGTCCGTTAGTTTCCAACAACAAGAAGAAAAGCAGCAAGAAAAGCGCCAGGTTCAGCGATGAGGTGGAGGATTACGTGATGAATAAATTACGGCAACTTAGAAAAAACCATGAAAGAAGATAA

Protein sequence

>Msa1422980

MEISQEKENHHHQEIWSETESNGSRSTRVGFSGSLSGPLSGPLVSNNKKKSSKKSARFSDEVEDYVMNKLRQLRKNHERR*